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批量重命名文件和文件夾是一個經常被問到的問題，但經過一番搜索之後，我認爲沒有一個類似於我的。使用「索引」重命名批量（基本名稱）文件/文件夾
背景：我們派一些生物樣品返回具有獨特名稱的文件和文本格式包含表服務供應商，其中包括信息，文件名和源自它的樣本：
head samples.txt
fq_file Sample_ID Sample_name Library_ID FC_Number Track_Lanes_Pos
L2369_Track-3885_R1.fastq.gz S1746_B_7_t B 7 t L2369_B_7_t 163 6
L2349_Track-3865_R1.fastq.gz S1726_A_3_t A 3 t L2349_A_3_t 163 5
L2354_Track-3870_R1.fastq.gz S1731_A_GFP_c A GFP c L2354_A_GFP_c 163 5
L2377_Track-3893_R1.fastq.gz S1754_B_7_c B 7 c L2377_B_7_c 163 7
L2362_Track-3878_R1.fastq.gz S1739_B_GFP_t B GFP t L2362_B_GFP_t 163 6
目錄結構（34個目錄）：
L2369_Track-3885_
accepted_hits.bam
deletions.bed
junctions.bed
logs
accepted_hits.bam.bai
insertions.bed
left_kept_reads.info
L2349_Track-3865_
accepted_hits.bam
deletions.bed
junctions.bed
logs
accepted_hits.bam.bai
insertions.bed
left_kept_reads.info
目標：因爲文件名是毫無意義的，很難解釋，我要重命名.bam結束（保持後綴）的文件和文件夾與通信樣品名稱，以更合適的方式重新排序。結果應該是這樣的：
7_t_B
7_t_B..bam
deletions.bed
junctions.bed
logs
7_t_B.bam.bai
insertions.bed
left_kept_reads.info
3_t_A
3_t_A.bam
deletions.bed
junctions.bed
logs
accepted_hits.bam.bai
insertions.bed
left_kept_reads.info
我砍死在一起使用bash和python（新手）的解決方案，但感覺過度設計。問題是，是否有更簡單/更優雅的方式來實現這一點，我錯過了？解決方案可以使用python，bash和R.也可以awk，因爲我正在嘗試學習它。作爲一個相對的初學者確實會讓事情變得複雜。
這是我的解決方案：
的包裝紙把它全部到位，並給出了工作流程的一個想法：
#! /bin/bash
# select columns of interest and write them to a file - basenames
tail -n +2 samples.txt | cut -d$'\t' -f1,3 >> BAMfilames.txt
# call my little python script that creates a new .sh with the renaming commmands
./renameBamFiles.py
# finally do the renaming
./renameBam.sh
# and the folders to
./renameBamFolder.sh
renameBamFiles.py：
#! /usr/bin/env python
import re
# Read in the data sample file and create a bash file that will remane the tophat output
# the reanaming will be as follows:
# mv L2377_Track-3893_R1_ L2377_Track-3893_R1_SRSF7_cyto_B
#
# Set the input file name
# (The program must be run from within the directory
# that contains this data file)
InFileName = 'BAMfilames.txt'
### Rename BAM files
# Open the input file for reading
InFile = open(InFileName, 'r')
# Open the output file for writing
OutFileName= 'renameBam.sh'
OutFile=open(OutFileName,'a') # You can append instead with 'a'
OutFile.write("#! /bin/bash"+"\n")
OutFile.write(" "+"\n")
# Loop through each line in the file
for Line in InFile:
## Remove the line ending characters
Line=Line.strip('\n')
## Separate the line into a list of its tab-delimited components
ElementList=Line.split('\t')
# separate the folder string from the experimental name
fileroot=ElementList[1]
fileroot=fileroot.split()
# create variable names using regex
folderName=re.sub(r'^(.*)(\_)(\w+).*', r'\1\2\3\2', ElementList[0])
folderName=folderName.strip('\n')
fileName = "%s_%s_%s" % (fileroot[1], fileroot[2], fileroot[0])
command= "for file in %s/accepted_hits.*; do mv $file ${file/accepted_hits/%s}; done" % (folderName, fileName)
print command
OutFile.write(command+"\n")
# After the loop is completed, close the files
InFile.close()
OutFile.close()
### Rename folders
# Open the input file for reading
InFile = open(InFileName, 'r')
# Open the output file for writing
OutFileName= 'renameBamFolder.sh'
OutFile=open(OutFileName,'w')
OutFile.write("#! /bin/bash"+"\n")
OutFile.write(" "+"\n")
# Loop through each line in the file
for Line in InFile:
## Remove the line ending characters
Line=Line.strip('\n')
## Separate the line into a list of its tab-delimited components
ElementList=Line.split('\t')
# separate the folder string from the experimental name
fileroot=ElementList[1]
fileroot=fileroot.split()
# create variable names using regex
folderName=re.sub(r'^(.*)(\_)(\w+).*', r'\1\2\3\2', ElementList[0])
folderName=folderName.strip('\n')
fileName = "%s_%s_%s" % (fileroot[1], fileroot[2], fileroot[0])
command= "mv %s %s" % (folderName, fileName)
print command
OutFile.write(command+"\n")
# After the loop is completed, close the files
InFile.close()
OutFile.close()
RenameBam.sh - 由以前的python腳本創建：
#! /bin/bash
for file in L2369_Track-3885_R1_/accepted_hits.*; do mv $file ${file/accepted_hits/7_t_B}; done
for file in L2349_Track-3865_R1_/accepted_hits.*; do mv $file ${file/accepted_hits/3_t_A}; done
for file in L2354_Track-3870_R1_/accepted_hits.*; do mv $file ${file/accepted_hits/GFP_c_A}; done
(..)
重命名renameBamFolder.sh非常相似：
mv L2369_Track-3885_R1_ 7_t_B
mv L2349_Track-3865_R1_ 3_t_A
mv L2354_Track-3870_R1_ GFP_c_A
mv L2377_Track-3893_R1_ 7_c_B
自從我學習，我覺得的這樣做，並思考如何做到這一點的不同方法的一些示例，將是非常有用的。
使用Python生成bash似乎有點沒有意義。我會說選擇一種語言或其他語言，然後使用它。如果你不習慣，Python也許不那麼神祕。 – 2013-02-20 13:11:30