Mercurial > repos > iuc > irma
diff createMissingFiles.py @ 1:736090e99c59 draft
planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402
| author | iuc |
|---|---|
| date | Wed, 22 Jan 2025 14:10:33 +0000 |
| parents | 3d86c05cd838 |
| children |
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--- a/createMissingFiles.py Sat Nov 09 13:53:38 2024 +0000 +++ b/createMissingFiles.py Wed Jan 22 14:10:33 2025 +0000 @@ -3,8 +3,8 @@ import subprocess dirPrefix = "resultDir/" -expectedSegments = ["A_MP", "A_NP", "A_HA", "A_PB1", - "A_PB2", "A_NA", "A_PA", "A_NS"] +expectedSegments = {"A_MP": 7, "A_NP": 5, "A_HA": 4, "A_PB1": 2, + "A_PB2": 1, "A_NA": 6, "A_PA": 3, "A_NS": 8} def renameSubtypeFiles(identifier): @@ -19,7 +19,7 @@ for file in os.listdir(dirPrefix): if file.endswith(".fasta"): presentSegments.append(file.split('.')[0]) - return [segment for segment in expectedSegments + return [segment for segment in expectedSegments.keys() if segment not in presentSegments] @@ -56,8 +56,13 @@ f.write(vcfHeader) +def writeEmptyAmendedFasta(identifier): + # irma names these files like: resultDir/amended_consensus/resultDir_<segNr>.fa + open(dirPrefix + "amended_consensus/resultDir_" + str(expectedSegments[identifier]) + ".fa", 'x').close() + + def samtoolsSortAllBam(): - for segment in expectedSegments: + for segment in expectedSegments.keys(): os.rename(dirPrefix + segment + ".bam", dirPrefix + segment + "_unsorted.bam") cmd = ['samtools', 'sort', dirPrefix + segment + "_unsorted.bam"] @@ -76,4 +81,5 @@ writeEmptyBam(segment, bamHeader) writeEmptyFasta(segment) writeEmptyVcf(segment, vcfHeader) + writeEmptyAmendedFasta(segment) samtoolsSortAllBam()