如何在Python中跳過讀取輸入文件的第一行

Question

我正在嘗試編寫一個腳本，該腳本將自動處理包含DNA序列的文件並將其轉換為蛋白質序列。 到目前為止，我唯一遇到的麻煩是，為了讓我的腳本處理文件內文件，我需要以某種方式省略第一行。

我的代碼如下所示：

#!/usr/bin/python

### This script will translate in all three frames ###

import glob
from Bio.Seq import *
from Bio.Alphabet import generic_dna

print "Please drag in the directory to be processed: "
folder = raw_input().replace(" ","")
file = glob.glob(str(folder) + "/" + '*.seq')

for i in file:

        with open (i, "r") as myfile:

                ### Need to somehow remove / read over the first line of the input...###

                seq = myfile.read().replace(" ", "").replace("\n", "")

        x = 0

        output = open(i + ".tran", "w+")

        while x < 3:
                cd = Seq(seq[x:], generic_dna)
                qes = seq[::-1]
                cdr = Seq(qes[x:], generic_dna)
                error = cd.translate().count('*')
                reverror = cdr.translate().count('*')
                output.write(str(cd.translate()) + "\nStops: " + str(error) + "\n\n")
                output.write("Reverse\n" + str(cdr.translate()) + "\nStops: " + str(reverror) + "\n\n")
                x += 1

我的輸入文件可能看起來像這樣

>G2-pBAD-Forward_A11.ab1
NNNNNNNNNNCNNNCNGNNGCTTTTTATCGCAACTCTCTACTGTTTCTCCATACCCGTTTTTTTGGGCTAGCGAATTCGA
GCTCGAAATAATTTTGTTTAACTTTAAGAAGGAGATATACATATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGT
ACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCAAGCTTGGCTGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACA
GATTAAATCAGAACGCAGAAGCGGTCTGATAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCA
TGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCA
TCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTA
GGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACT
GCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTTTGTTTATTTTTCT
AAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATG
AGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCT
GGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCAGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCA
ACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGGTTTATT
GCTGATAAATCTGGAGCCGGTGAGCGTGNTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTTCCCGTAT
CGNANTTNNCTACACGAN

我需要的是一種優雅的方法來刪除包含“>”的第一行。

Answer 1

您可以使用SeqIO ：

with open(i) as myfile:
    for record in SeqIO.parse(myfile, "fasta"):
       print record.id
       print record.seq  

record.seq會給你的序列， record.id會給你的ID，如果你只擁有或者希望在每一個序列你可以調用next：

with open(i) as myfile:
    print(next(SeqIO.parse(myfile, "fasta"))).seq

我在您的輸入中看不到任何空格，所以我不確定替換將如何工作，這會將序列輸出為單個字符串。

輸出：

NNNNNNNNNNCNNNCNGNNGCTTTTTATCGCAACTCTCTACTGTTTCTCCATACCCGTTTTTTTGGGCTAGCGAATTCGAGCTCGAAATAATTTTGTTTAACTTTAAGAAGGAGATATACATATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCAAGCTTGGCTGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCAGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGNTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTTCCCGTATCGNANTTNNCTACACGAN

您還可以使用range而不是while循環，並將字母傳遞給SeQIO：

for record in SeqIO.parse(myfile, "fasta",generic_dna)
    ...
for x in range(3):
       ....

這應該更接近您想要的：

from Bio import SeqIO
from Bio.Alphabet import generic_dna
from Bio.Seq import Seq


folder = raw_input().replace(" ","")
files = glob.glob(folder + "/" + '*.seq')

for i in files:
    with open(i) as myfile:
            seq = next(SeqIO.parse(myfile, "fasta", generic_dna)).seq
            qes = seq[::-1]
            with open("{}.tran".format(i), "w+") as output:
                 for x in range(3):
                     cd = seq[x:]
                     cdr = qes[x:]
                     error = seq.translate().count('*')
                     reverror = cdr.translate().count('*')
                     output.write("{}\nstops: {}\n\n".format(cd.translate(), error))
                     output.write("Reverse: {}\nStops: {}\n\n ".format(cdr.translate(), reverror))

哪個輸出：

XXXXXXXFLSQLSTVSPYPFFWASEFELEIILFNFKKEIYI*L**NELLPCLLYC*WAGR*MPGQAWLFWRMREDFQPDTD*IRTQKRSDKTEFAWRQ*RGGPT*PHAELRSETP*RRW*CGVSPCESRELPGIK*NERLSRKTGPFVLSVVCR*TLS*VGQIRRERI*TLRSNGPEGGGQDARHKLPGIKLSRRPS*RMAFLRFYKLFCLFF*IHSNMYPLMRQ*P**MLQ*Y*KRKSMSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGAANY*LANYLL*LPGNN**TGWRRIKLQDHFCARPFRLAGFIADKSGAGERXLAVSLQHWGQMVSPSRIXXXYT
stops: 25

Reverse: XHIXXXYALPEW*TGVTTLLWRSXASGRGLNSRYLGRSAFPARVFTRTLK*AEVGQIINNGPSISFIKRSIIKRRGLTRSRRK*KWSQRPTRFCPSVLRRFFPYSRCAFTTYEYEKEKVIITS*IVPITEYSPMYKLT*IFLFVFSNIFAFFR*AVLPEDELNYGPSNTARRTGGGRPGNEALQV*ARAA*TG*VLSQVAVCCLFCFPGQKADSESKINYGPSRDESVPLWGVMVAAMPQSEDSSRTPVHPGGAMTAVRLRQNSLAKTQD*IRHSPTFRRE*AVLSVRTGP*MAGRVVVMSFVPLLSKVMLVYI*RKNFNLF**SSSLSDRVFLPIPLCHLSTLFFXXXXXX
Stops: 15

 XXXXXXAFYRNSLLFLHTRFFGLANSSSK*FCLTLRRRYTYDCNETSYYPVCCTADGLVGKCLVKLGCFGG*EKIFSLIQIKSERRSGLIKQNLPGGSSAVVPPDPMPNSEVKRRSADGSVGSPHARVGNCQASNKTKGSVERLGLSFYLLFVGERSPE*DKSAGSGFERCEATARRVAGRTPAINCQASN*AEGHPDGWPFCVSTNSFVYFSKYIQICIRS*DNNPDKCFNNIEKGRV*VFNISVSPLFPFLRHFAFLFLLTQKRW*K*KMLKISWVQQTINWRTTYSSFPATINRLDGGG*SCRTTSALGPSGWLGLLLINLEPVSVXSRYHCSTGARW*ALPVSXXXTR
stops: 25

Reverse: STSXXAMPFPNGRPGSRRYYGALVRVAEV*IVVIWVGRPSRLASSPGR*NRRR*VR*LTTALRSHSSSGQLSNDVG*LEVVENESGRKDPLVFVLPFYGVFSLIPAVPLQLMSMRRKKL**LRK*SQ*QSTRLCINLHKSFYLFSQTSLRFSGRQSYRKTN*TTDRQIPPAGRAVGGPATKRCKFRRGPPKQDESSRKWLFVVYFAFRVRKLTRKAK*TTDRQGMRAYPSGV*W*PRCRKVKTQAVPQSTLVAR*RRSV*DKIVWRRRKTKLDIVRLLEESRRFCRFELVRKWLVG*SSCRLSHY*AK*C*YTYRGRISICFNKARA*AIGFFCPYLFVISQRYFSXXXXXX
Stops: 20

 XXXXXXLFIATLYCFSIPVFLG*RIRARNNFV*L*EGDIHMIVMKRVITLFAVLLMGWSVNAWSSLAVLADERRFSA*YRLNQNAEAV**NRICLAAVARWSHLTPCRTQK*NAVAPMVVWGLPMRE*GTARHQIKRKAQSKDWAFRFICCLSVNALLSRTNPPGADLNVAKQRPGGWRAGRPP*TARHQIKQKAILTDGLFAFLQTLLFIFLNTFKYVSAHETITLINASIILKKEEYEYSTFPCRPYSLFCGILPSCFCSPRNAGESKRC*RSVGCSKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWVYC**IWSR*AXSRGIIAALGPDGKPFPYRXXLHX
stops: 25

Reverse: AHXXXLCPSRMVDRGHDVTMALXCEWPRSK*SLFGSVGLPGSRLHQDVEIGGGRSDN*QRPFDLIHQAVNYQTTWVD*KS*KMKVVAKTHSFLSFRFTAFFPLFPLCLYNL*V*EGKSYNNFVNSPNNRVLAYV*TYINLFICFLKHLCVFPVGSPTGRRIKLRTVKYRPQDGRWEARQRSVASLGEGRLNRMSPLASGCLLSILLSGSES*LGKQNKLRTVKG*ERTPLGCDGSRDAAK*RLKPYPSPPWWRDDGGPFKTK*SGEDARLN*T*SDF*KRVGGFVGSNWSVNGWSGSRHVVCPIIEQSNVSIHIEEEFQFVLIKLELKRSGFFAHTSLSSLNAIFRXXXXXX
Stops: 14

盡管出現警告，因為您的序列不是三的倍數

Answer 2

starting = True
lines = []
with open (i, "r") as myfile:
    for line in myfile:
        if starting:
            starting = False
            continue
        lines.append(line)

# now you have all the lines except the first one in "lines"     

Answer 3

當您閱讀文件時，請檢查該行的第一個字符是否為'>'。 如果是這樣，則只需閱讀該行並跳過它。 就像上面提到的注釋一樣，您可能希望在每次讀一行時都進行檢查，以便知道您是在處理新序列還是相同序列，因為您的文件可能具有多個序列。

該鏈接將為您提供有關讀取python文件的所有文檔。 https://docs.python.org/2/tutorial/inputoutput.html