如何在與python匹配后打印行？

Question

我有一個文件，有幾行（我只顯示其中的兩行）：

UniRef90_A0A0K2VG56 UniRef90_A0A0P5UY87 
UniRef90_A0A095VQ09 UniRef90_A0A0C1UI80 UniRef90_A0A1M4ZSK2

和另一個文件（我只顯示文件的一些行）：

>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

對於第一個文件的每一行，我需要將Uniref90_XXXXXX ID 與第二個文件的Uniref90_XXXXXX ID 進行Uniref90_XXXXXX 。 匹配完成后，我需要將序列（字母 ...TNGSGQATS.... = 序列）恢復到相應的 ID。

例如，第一個文件的第一行有 2 個 Uniref90_XXXXX ID，我想得到這樣的輸出：

>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

我需要為我的第一個文件的每一行都這樣做。

Answer 1

因此，您似乎需要根據第一個文件中的順序對Uniref90_XXXXXX進行排序。

這里UniRef_ids.txt是你的第一個文件， UniRef_data.txt是你的第二個文件， UniRef_data_ordered.txt是輸出文件。

我注意到每個Uniref90_XXXXXX似乎都以>開頭並繼續，跨越可變數量的行，直到下一個>或者，我假設，文件末尾。

我只處理了一個異常：如果Uniref90_XXXXXX出現在您的第一個文件中，但沒有出現在您的第二個文件中。 它只是向您的控制台（而不是您的文件）打印警告。

如果其余文件的格式不同，這可能不起作用。 同樣，如果您的文件有幾 GB，我的方法可能不合適，因為我將第二個文件的全部內容讀入內存。

# 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

---

是否可以為循環的每次迭代創建單獨的文件？ 我的意思是，對於第一個文件的每一行，我想創建一個帶有 ID 和相應序列的文件？

是的，這是可能的。 我們只需要打開輸出文件並在遍歷第一個文件中的行的 for 循環中編寫代碼，並為每個文件指定一個唯一的名稱。

# 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...")

順便說一下，這是生成文件名的代碼：

f"UniRef_data_by_id_row_{i:03}.txt"

f前綴告訴 Python 它是一個f-string 。 它評估{}的內容並返回一個字符串。 在:之前是值，之后是格式說明符。 在這種情況下，我的格式說明符 0-pads i的寬度為 3，給我的文件名如下：

UniRef_data_by_id_row_001.txt
UniRef_data_by_id_row_999.txt

這樣，在文件管理器中對文件進行排序非常容易。

您可以對文件進行不同的命名。 例如，如果您不需要下划線，並且想用空格而不是 0 填充數字：

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