如何在与python匹配后打印行？

Question

I have a file, with several lines (I only show two of them):

UniRef90_A0A0K2VG56 UniRef90_A0A0P5UY87 
UniRef90_A0A095VQ09 UniRef90_A0A0C1UI80 UniRef90_A0A1M4ZSK2

and another file (I only show some lines of the file) :

>UniRef90_A0A095VQ09 - Cluster: LOW QUALITY PROTEIN: titin
MTTKAPTFTQPLQSVVALEGSAATFEAHISGSPVPEVSWYRDGQVLSAATLPGVQISFSD
GRAKLMIPAVAAGHSGRYTLQATNGSGQATSTAELLVTAETAPPNFSQRLQSTTARQGSQ
VRLDVRVTGIPTPVVKFYRDRAEIQSSPDFQILQEGDLYSLIIAEAYPEDSGTYSVNATN
>UniRef90_A0A0K2VG56 - Cluster: titin isoform X29
MATQAPTFTQPLQSVVVLEGSTATFEAHISGFPVPEVSWFRDGQVISTSTLPGVQISFSD
GRAKLMIPAVTKANSGRYSLRATNGSGQATSTAELLVKAETAPPNFVQRLQSMTVRQGSQ
VRLQVRVTGIPTPVVKFYRDGAEIQSSLDFQISQEGELYSLLIVEAYPEDSGTYSVNATN
SVGRATSTAELLVQGEEVVPAKKTKTIVSTAQISKSRETRIEKKIEAHFDARSIATVEMV
IDGAAGQELPHKTPPRIPLKPKSRSPTPPSIAAKAQLARQQSPSPIRHSPSPVRHVRAPT
>UniRef90_A0A0C1UI80 - Cluster: LOW QUALITY PROTEIN: lafev
GRAKLMIPAVTKANSGRYSLRATNGSGQATSTAELLVKAETAPPNFVQRLQSMTVRQGSQ
VRLQVRVTGIPTPVVKFYRDGAEIQSSLDFQISQEGLARQQSPSPIRHSPSPVRHVRAPT
>UniRef90_A0A0P5UY87 - Cluster: titin isoform X4
VRLQVRVTGIPTPVVKFYRDGAEIQSSLDFQISQEGELYSLLIVEAYPEDSGTYSVNATN
SVGRATSTAELLVQGEEVVPAKKTKTIVSTAQISKSRETRIEKKIEAHFDARSIATVEMV
GRAKLMIPAVAAGHSGRYTLQATNGSGQATSTAELLVTAETAPPNFSQRLQSTTARQGSQ
>UniRef90_A0A1M4ZSK2  - Cluster: titin isoform X54
SVGRATSTAELLVQGEEVVPAKKTKTIVSTSTAELLVTAETAPPNFSQRLQSTTARQGSQ
SVGRATSTAELLVQGEEVVPAKKTKTIVSTAQISKSRETRIEKKIEAHFDARSIATVEMV
IDGAAGQELPHKTPPRIPLKPKSRSPTPPSIAAKAQLARQQSPSPIRHSPSPVRHVRAPT

I need to match, for each line of my first file, the Uniref90_XXXXXX ID with Uniref90_XXXXXX ID of the second file. When the match is done, I need to get back the sequence (the letters ...TNGSGQATS.... = sequences) to the corresponding ID.

For example, there are 2 Uniref90_XXXXX IDs in the first row of the first file, I woud like to get an output like this :

>UniRef90_A0A0K2VG56 - Cluster: titin isoform X29
MATQAPTFTQPLQSVVVLEGSTATFEAHISGFPVPEVSWFRDGQVISTSTLPGVQISFSD
GRAKLMIPAVTKANSGRYSLRATNGSGQATSTAELLVKAETAPPNFVQRLQSMTVRQGSQ
VRLQVRVTGIPTPVVKFYRDGAEIQSSLDFQISQEGELYSLLIVEAYPEDSGTYSVNATN
SVGRATSTAELLVQGEEVVPAKKTKTIVSTAQISKSRETRIEKKIEAHFDARSIATVEMV
IDGAAGQELPHKTPPRIPLKPKSRSPTPPSIAAKAQLARQQSPSPIRHSPSPVRHVRAPT   ##first ID of the first line
>UniRef90_A0A0P5UY87 - Cluster: titin isoform X4
VRLQVRVTGIPTPVVKFYRDGAEIQSSLDFQISQEGELYSLLIVEAYPEDSGTYSVNATN   
SVGRATSTAELLVQGEEVVPAKKTKTIVSTAQISKSRETRIEKKIEAHFDARSIATVEMV
GRAKLMIPAVAAGHSGRYTLQATNGSGQATSTAELLVTAETAPPNFSQRLQSTTARQGSQ   ##second ID of the first line

And I need to do that for each row of my first file.

Answer 1

So you seem to need to order Uniref90_XXXXXX s according to their order in the first file.

Here UniRef_ids.txt is your first file, UniRef_data.txt is your second file, and UniRef_data_ordered.txt is the output file.

I noticed each Uniref90_XXXXXX appears to start with a > and continues, spanning a variable number of lines, until the next > or, I assume, the end of file.

I have only handled one exception: if a Uniref90_XXXXXX appears your first file, but not your second. It merely prints a warning to your console (not your file).

If the rest of your files are formatted differently, this might not work. Similarly, if your files are several gigabytes, my approach may not be appropriate, as I read into memory the entire contents of your second file.

# We first go through the second file, get all the Uniref90_XXXXXX IDs, and 
# put their sequences (including the Uniref90_XXXXXX header line) into a dict.
# A sequence can be accessed like so: uniref_dict["UniRef90_A0A0K2VG56"]
with open("UniRef_data.txt", "rt") as f:
    data = f.read()

uniref_dict = {}
for uniref in [f">{chunk.rstrip()}" for chunk in data.split(">")]:
    uniref_id = uniref[1:uniref.find(" ")]
    uniref_dict[uniref_id] = uniref

# Then we go through the first file, line by line, id by id, and write to 
# a new file the corresponding sequence (again, including the Uniref90_XXXXXX 
# header line, as per your output) and append the Uniref90_XXXXXX at the end.
with open("UniRef_ids.txt", "rt") as fin:
    with open("UniRef_data_ordered.txt", "wt") as fout:
        for line in fin:
            line = line.rstrip()
            uniref_ids = line.split(" ")
            for uniref_id in uniref_ids:
                try:
                    fout.write("{} ##{}\n".format(uniref_dict[uniref_id], uniref_id))
                except KeyError as e:
                    print(f"uniref_id '{uniref_id}' found in id file but not data file. Continuing...")

UniRef_data_ordered.txt:

>UniRef90_A0A0K2VG56 - Cluster: titin isoform X29
MATQAPTFTQPLQSVVVLEGSTATFEAHISGFPVPEVSWFRDGQVISTSTLPGVQISFSD
GRAKLMIPAVTKANSGRYSLRATNGSGQATSTAELLVKAETAPPNFVQRLQSMTVRQGSQ
VRLQVRVTGIPTPVVKFYRDGAEIQSSLDFQISQEGELYSLLIVEAYPEDSGTYSVNATN
SVGRATSTAELLVQGEEVVPAKKTKTIVSTAQISKSRETRIEKKIEAHFDARSIATVEMV
IDGAAGQELPHKTPPRIPLKPKSRSPTPPSIAAKAQLARQQSPSPIRHSPSPVRHVRAPT ##UniRef90_A0A0K2VG56
>UniRef90_A0A0P5UY87 - Cluster: titin isoform X4
VRLQVRVTGIPTPVVKFYRDGAEIQSSLDFQISQEGELYSLLIVEAYPEDSGTYSVNATN
SVGRATSTAELLVQGEEVVPAKKTKTIVSTAQISKSRETRIEKKIEAHFDARSIATVEMV
GRAKLMIPAVAAGHSGRYTLQATNGSGQATSTAELLVTAETAPPNFSQRLQSTTARQGSQ ##UniRef90_A0A0P5UY87
>UniRef90_A0A095VQ09 - Cluster: LOW QUALITY PROTEIN: titin
MTTKAPTFTQPLQSVVALEGSAATFEAHISGSPVPEVSWYRDGQVLSAATLPGVQISFSD
GRAKLMIPAVAAGHSGRYTLQATNGSGQATSTAELLVTAETAPPNFSQRLQSTTARQGSQ
VRLDVRVTGIPTPVVKFYRDRAEIQSSPDFQILQEGDLYSLIIAEAYPEDSGTYSVNATN ##UniRef90_A0A095VQ09
>UniRef90_A0A0C1UI80 - Cluster: LOW QUALITY PROTEIN: lafev
GRAKLMIPAVTKANSGRYSLRATNGSGQATSTAELLVKAETAPPNFVQRLQSMTVRQGSQ
VRLQVRVTGIPTPVVKFYRDGAEIQSSLDFQISQEGLARQQSPSPIRHSPSPVRHVRAPT ##UniRef90_A0A0C1UI80
>UniRef90_A0A1M4ZSK2  - Cluster: titin isoform X54
SVGRATSTAELLVQGEEVVPAKKTKTIVSTSTAELLVTAETAPPNFSQRLQSTTARQGSQ
SVGRATSTAELLVQGEEVVPAKKTKTIVSTAQISKSRETRIEKKIEAHFDARSIATVEMV
IDGAAGQELPHKTPPRIPLKPKSRSPTPPSIAAKAQLARQQSPSPIRHSPSPVRHVRAPT ##UniRef90_A0A1M4ZSK2

---

is it possible to create separate files for each iteration of the loop? I mean, for each row of the first file, I would like to create a file with the ID and the corresponding sequences?

Yes, that's possible. We just need to put the output file open and writing code inside the for loop that goes over the rows in the first file, and give each file a unique name.

# We first go through the second file, get all the Uniref90_XXXXXX IDs, and 
# put their sequences (including the Uniref90_XXXXXX header line) into a dict.
# A sequence can be accessed like so: uniref_dict["UniRef90_A0A0K2VG56"]
with open("UniRef_data.txt", "rt") as f:
    data = f.read()

uniref_dict = {}
for uniref in [f">{chunk.rstrip()}" for chunk in data.split(">")]:
    uniref_id = uniref[1:uniref.find(" ")]
    uniref_dict[uniref_id] = uniref

# Then we go through the first file, line by line, and write to a new  
# file the ids and their corresponding sequences (again, including the 
# Uniref90_XXXXXX header line, as per your output)
with open("UniRef_ids.txt", "rt") as fin:
    # Each iteration of this for loop is a new line of Uniref90_XXXXXX ids,
    # so we've moved the file writing code inside of this loop.
    # enumerate gives us a counter - i - that starts at 1, and increments by 1
    # after each iteration. We use this to give each file a unique name.
    for i, line in enumerate(fin, start=1):
        line = line.rstrip()
        uniref_ids = line.split(" ")
        with open(f"UniRef_data_by_id_row_{i:03}.txt", "wt") as fout:
            for uniref_id in uniref_ids:
                try:
                    fout.write(uniref_dict[uniref_id] + "\n")
                except KeyError as e:
                    print(f"uniref_id '{uniref_id}' found in id file but not data file. Continuing...")

By the way, this is the code that generates our filenames:

f"UniRef_data_by_id_row_{i:03}.txt"

The f prefix tells Python it's an f-string . It evaluates what's in the {} s and returns a string. Before the : is the value , and after are the format specifiers . In this case, my format specifiers 0-pads i to a width of 3, giving me filenames like:

UniRef_data_by_id_row_001.txt
UniRef_data_by_id_row_999.txt

That way, it's very easy to sort the files in your file manager.

You can name the files differently. For example, if you don't want underscores, and you want to pad the number with spaces instead of 0s:

f"UniRef Data Ordered by ID - Row {i: >4}.txt"

UniRef Data Ordered by ID - Row    1.txt
UniRef Data Ordered by ID - Row 9999.txt